1
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Abu Hassan A, Hanževački M, Pordea A. Computational investigation of cis-1,4-polyisoprene binding to the latex-clearing protein LcpK30. PLoS One 2024; 19:e0302398. [PMID: 38748648 PMCID: PMC11095694 DOI: 10.1371/journal.pone.0302398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 04/02/2024] [Indexed: 05/19/2024] Open
Abstract
Latex clearing proteins (Lcps) catalyze the oxidative cleavage of the C = C bonds in cis-1,4-polyisoprene (natural rubber), producing oligomeric compounds that can be repurposed to other materials. The active catalytic site of Lcps is buried inside the protein structure, thus raising the question of how the large hydrophobic rubber chains can access the catalytic center. To improve our understanding of hydrophobic polymeric substrate binding to Lcps and subsequent catalysis, we investigated the interaction of a substrate model containing ten carbon-carbon double bonds with the structurally characterized LcpK30, using multiple computational tools. Prediction of the putative tunnels and cavities in the LcpK30 structure, using CAVER-Pymol plugin 3.0.3, fpocket and Molecular Dynamic (MD) simulations provided valuable insights on how substrate enters from the surface to the buried active site. Two dominant tunnels were discovered that provided feasible routes for substrate binding, and the presence of two hydrophobic pockets was predicted near the heme cofactor. The larger of these pockets is likely to accommodate the substrate and to determine the size distribution of the oligomers. Protein-ligand docking was carried out using GOLD software to predict the conformations and interactions of the substrate within the protein active site. Deeper insight into the protein-substrate interactions, including close-contacts, binding energies and potential cleavage sites in the cis-1,4-polyisoprene, were obtained from MD simulations. Our findings provide further justification that the protein-substrate complexation in LcpK30 is mainly driven by the hydrophobic interactions accompanied by mutual conformational changes of both molecules. Two potential binding modes were identified, with the substrate in either extended or folded conformations. Whilst binding in the extended conformation was most favorable, the folded conformation suggested a preference for cleavage of a central double bond, leading to a preference for oligomers with 5 to 6 C = C bonds. The results provide insight into further enzyme engineering studies to improve catalytic activity and diversify the substrate and product scope of Lcps.
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Affiliation(s)
- Aziana Abu Hassan
- Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Marko Hanževački
- Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
| | - Anca Pordea
- Faculty of Engineering, University of Nottingham, Nottingham, United Kingdom
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2
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Platonov M, Maximyuk O, Rayevsky A, Hurmach V, Iegorova O, Naumchyk V, Bulgakov E, Cherninskyi A, Ozheredov D, Ryabukhin SV, Krishtal O, Volochnyuk DM. 4-(Azolyl)-Benzamidines as a Novel Chemotype for ASIC1a Inhibitors. Int J Mol Sci 2024; 25:3584. [PMID: 38612396 PMCID: PMC11011685 DOI: 10.3390/ijms25073584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 03/03/2024] [Accepted: 03/13/2024] [Indexed: 04/14/2024] Open
Abstract
Acid-sensing ion channels (ASICs) play a key role in the perception and response to extracellular acidification changes. These proton-gated cation channels are critical for neuronal functions, like learning and memory, fear, mechanosensation and internal adjustments like synaptic plasticity. Moreover, they play a key role in neuronal degeneration, ischemic neuronal injury, seizure termination, pain-sensing, etc. Functional ASICs are homo or heterotrimers formed with (ASIC1-ASIC3) homologous subunits. ASIC1a, a major ASIC isoform in the central nervous system (CNS), possesses an acidic pocket in the extracellular region, which is a key regulator of channel gating. Growing data suggest that ASIC1a channels are a potential therapeutic target for treating a variety of neurological disorders, including stroke, epilepsy and pain. Many studies were aimed at identifying allosteric modulators of ASIC channels. However, the regulation of ASICs remains poorly understood. Using all available crystal structures, which correspond to different functional states of ASIC1, and a molecular dynamics simulation (MD) protocol, we analyzed the process of channel inactivation. Then we applied a molecular docking procedure to predict the protein conformation suitable for the amiloride binding. To confirm the effect of its sole active blocker against the ASIC1 state transition route we studied the complex with another MD simulation run. Further experiments evaluated various compounds in the Enamine library that emerge with a detectable ASIC inhibitory activity. We performed a detailed analysis of the structural basis of ASIC1a inhibition by amiloride, using a combination of in silico approaches to visualize its interaction with the ion pore in the open state. An artificial activation (otherwise, expansion of the central pore) causes a complex modification of the channel structure, namely its transmembrane domain. The output protein conformations were used as a set of docking models, suitable for a high-throughput virtual screening of the Enamine chemical library. The outcome of the virtual screening was confirmed by electrophysiological assays with the best results shown for three hit compounds.
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Affiliation(s)
- Maksym Platonov
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Zabolotnogo Str., 150, 03143 Kyiv, Ukraine; (M.P.); (V.H.)
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
| | - Oleksandr Maximyuk
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine; (O.M.); (O.I.); (A.C.); (O.K.)
| | - Alexey Rayevsky
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Zabolotnogo Str., 150, 03143 Kyiv, Ukraine; (M.P.); (V.H.)
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str., 2A, 04123 Kyiv, Ukraine;
| | - Vasyl Hurmach
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Zabolotnogo Str., 150, 03143 Kyiv, Ukraine; (M.P.); (V.H.)
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
| | - Olena Iegorova
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine; (O.M.); (O.I.); (A.C.); (O.K.)
| | - Vasyl Naumchyk
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, 01601 Kyiv, Ukraine
| | - Elijah Bulgakov
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str., 2A, 04123 Kyiv, Ukraine;
| | - Andrii Cherninskyi
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine; (O.M.); (O.I.); (A.C.); (O.K.)
| | - Danil Ozheredov
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Osypovskoho Str., 2A, 04123 Kyiv, Ukraine;
| | - Serhiy V. Ryabukhin
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, 01601 Kyiv, Ukraine
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Academik Kukhar Str., 02660 Kyiv, Ukraine
| | - Oleg Krishtal
- Bogomoletz Institute of Physiology, National Academy of Sciences of Ukraine, 4 Bogomoletz Str., 01024 Kyiv, Ukraine; (O.M.); (O.I.); (A.C.); (O.K.)
| | - Dmytro M. Volochnyuk
- Enamine Ltd., 78 Winston Churchill Str., 02660 Kyiv, Ukraine; (V.N.); (E.B.); (D.M.V.)
- Institute of High Technologies, Taras Shevchenko National University of Kyiv, Volodymyrska Street 60, 01601 Kyiv, Ukraine
- Institute of Organic Chemistry, National Academy of Sciences of Ukraine, 5 Academik Kukhar Str., 02660 Kyiv, Ukraine
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3
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Sirokha D, Rayevsky A, Gorodna O, Kalynovskyi V, Zelinska N, Samson O, Kwiatkowska K, Nef S, Jaruzelska J, Kusz-Zamelczyk K, Livshits L. Mutations in STARD8 (DLC3) May Cause 46,XY Gonadal Dysgenesis. Sex Dev 2024; 17:181-189. [PMID: 38447543 DOI: 10.1159/000537877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
INTRODUCTION 46,XY gonadal dysgenesis is a condition that is characterised by undeveloped testes in individuals with a male karyotype. Mutations in many genes that underlie this condition have been identified; however, there are still a considerable number of patients with an unknown genetic background. Recently, a mutation in the STARD8 X-linked gene in two sisters with 46,XY gonadal dysgenesis has been reported. It was localised within the START domain, whose homologue in Drosophila is responsible for maintaining testes integrity during their development. METHODS We analysed the potential pathogenicity of another STARD8 mutation, p.R887C, that was identified in a patient with 46,XY asymmetric gonadal dysgenesis. For this purpose, molecular dynamics simulations were performed. RESULTS These simulations revealed the full rearrangement of the helix containing the p.R887C substitution upstream from the START domain, which may cause STARD8 protein dysfunction and contribute to 46,XY gonadal dysgenesis. A comparison of the phenotypes of the three described 46,XY gonadal dysgenesis patients that harbour STARD8 mutations indicated that alterations of this gene can result in a partial or complete gonadal dysgenesis phenotype. CONCLUSION Based on these and previous results, it is reasonable to include STARD8 in gene panels for 46,XY gonadal dysgenesis.
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Affiliation(s)
- Dmytro Sirokha
- Department of Molecular Genetics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alexey Rayevsky
- Department of Molecular Genetics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Institute of Food Biotechnology and Genomics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Modeling, Enamine Ltd., Kyiv, Ukraine
| | - Olexandra Gorodna
- Department of Molecular Genetics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Vitalii Kalynovskyi
- Department of Pediatric Endocrinology, Ukrainian Scientific and Practical Center for Endocrine Surgery, Transplantation of Endocrine Organs and Tissues, Ministry of Health of Ukraine, Kyiv, Ukraine
| | - Nataliya Zelinska
- Department of Pediatric Endocrinology, Ukrainian Scientific and Practical Center for Endocrine Surgery, Transplantation of Endocrine Organs and Tissues, Ministry of Health of Ukraine, Kyiv, Ukraine
| | - Oksana Samson
- Endocrine Department, Shupyk National Healthcare University of Ukraine, Kyiv, Ukraine
| | | | - Serge Nef
- Department of Genetic Medicine and Development, Faculty of Medicine, University of Geneva Medical School, Geneva, Switzerland
| | | | | | - Ludmila Livshits
- Department of Molecular Genetics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
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4
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Špačková A, Bazgier V, Raček T, Sehnal D, Svobodová R, Berka K. Analysis and Visualization of Protein Channels, Tunnels, and Pores with MOLEonline and ChannelsDB 2.0. Methods Mol Biol 2024; 2836:219-233. [PMID: 38995543 DOI: 10.1007/978-1-0716-4007-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/13/2024]
Abstract
Channels, tunnels, and pores serve as pathways for the transport of molecules and ions through protein structures, thus participating to their functions. MOLEonline ( https://mole.upol.cz ) is an interactive web-based tool with enhanced capabilities for detecting and characterizing channels, tunnels, and pores within protein structures. MOLEonline has two distinct calculation modes for analysis of channel and tunnels or transmembrane pores. This application gives researchers rich analytical insights into channel detection, structural characterization, and physicochemical properties. ChannelsDB 2.0 ( https://channelsdb2.biodata.ceitec.cz/ ) is a comprehensive database that offers information on the location, geometry, and physicochemical characteristics of tunnels and pores within macromolecular structures deposited in Protein Data Bank and AlphaFill databases. These tunnels are sourced from manual deposition from literature and automatic detection using software tools MOLE and CAVER. MOLEonline and ChannelsDB visualization is powered by the LiteMol Viewer and Mol* viewer, ensuring a user-friendly workspace. This chapter provides an overview of user applications and usage.
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Affiliation(s)
- Anna Špačková
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Václav Bazgier
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Tomáš Raček
- Central European Institute of Technology (CEITEC), Masaryk University Brno, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Brno, Czech Republic
| | - David Sehnal
- Central European Institute of Technology (CEITEC), Masaryk University Brno, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Brno, Czech Republic
| | - Radka Svobodová
- Central European Institute of Technology (CEITEC), Masaryk University Brno, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Brno, Czech Republic
| | - Karel Berka
- Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic.
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5
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Morizumi T, Kim K, Li H, Govorunova EG, Sineshchekov OA, Wang Y, Zheng L, Bertalan É, Bondar AN, Askari A, Brown LS, Spudich JL, Ernst OP. Structures of channelrhodopsin paralogs in peptidiscs explain their contrasting K + and Na + selectivities. Nat Commun 2023; 14:4365. [PMID: 37474513 PMCID: PMC10359266 DOI: 10.1038/s41467-023-40041-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023] Open
Abstract
Kalium channelrhodopsin 1 from Hyphochytrium catenoides (HcKCR1) is a light-gated channel used for optogenetic silencing of mammalian neurons. It selects K+ over Na+ in the absence of the canonical tetrameric K+ selectivity filter found universally in voltage- and ligand-gated channels. The genome of H. catenoides also encodes a highly homologous cation channelrhodopsin (HcCCR), a Na+ channel with >100-fold larger Na+ to K+ permeability ratio. Here, we use cryo-electron microscopy to determine atomic structures of these two channels embedded in peptidiscs to elucidate structural foundations of their dramatically different cation selectivity. Together with structure-guided mutagenesis, we show that K+ versus Na+ selectivity is determined at two distinct sites on the putative ion conduction pathway: in a patch of critical residues in the intracellular segment (Leu69/Phe69, Ile73/Ser73 and Asp116) and within a cluster of aromatic residues in the extracellular segment (primarily, Trp102 and Tyr222). The two filters are on the opposite sides of the photoactive site involved in channel gating.
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Affiliation(s)
- Takefumi Morizumi
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Kyumhyuk Kim
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Hai Li
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Elena G Govorunova
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Oleg A Sineshchekov
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Yumei Wang
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Lei Zheng
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA
| | - Éva Bertalan
- Physikzentrum, RWTH-Aachen University, Aachen, Germany
| | - Ana-Nicoleta Bondar
- Faculty of Physics, University of Bucharest, Măgurele, Romania
- Institute of Computational Biomedicine (IAS-5/INM-9), Forschungszentrum Jülich, Jülich, Germany
| | - Azam Askari
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - Leonid S Brown
- Department of Physics and Biophysics Interdepartmental Group, University of Guelph, Guelph, ON, Canada
| | - John L Spudich
- Department of Biochemistry & Molecular Biology, Center for Membrane Biology, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX, USA.
| | - Oliver P Ernst
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
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6
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Ulbrich P, Waldner M, Furmanova K, Marques SM, Bednar D, Kozlikova B, Byska J. sMolBoxes: Dataflow Model for Molecular Dynamics Exploration. IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS 2023; 29:581-590. [PMID: 36155456 DOI: 10.1109/tvcg.2022.3209411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus, biochemists rely to a large extent only on quantitative analysis of geometric and physico-chemical properties. However, the usage of abstract methods to study inherently spatial data hinders the exploration and poses a considerable workload. sMolBoxes link quantitative analysis of a user-defined set of properties with interactive 3D visualizations. They enable visual explanations of molecular behaviors, which lead to an efficient discovery of biochemically significant parts of the MD simulation. sMolBoxes follow a node-based model for flexible definition, combination, and immediate evaluation of properties to be investigated. Progressive analytics enable fluid switching between multiple properties, which facilitates hypothesis generation. Each sMolBox provides quick insight to an observed property or function, available in more detail in the bigBox View. The case studies illustrate that even with relatively few sMolBoxes, it is possible to express complex analytical tasks, and their use in exploratory analysis is perceived as more efficient than traditional scripting-based methods.
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7
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Strom A, Shah R, Dolot R, Rogers MS, Tong CL, Wang D, Xia Y, Lipscomb JD, Wagner CR. Dynamic Long-Range Interactions Influence Substrate Binding and Catalysis by Human Histidine Triad Nucleotide-Binding Proteins (HINTs), Key Regulators of Multiple Cellular Processes and Activators of Antiviral ProTides. Biochemistry 2022; 61:2648-2661. [PMID: 36398895 PMCID: PMC9854251 DOI: 10.1021/acs.biochem.2c00506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Human histidine triad nucleotide-binding (hHINT) proteins catalyze nucleotide phosphoramidase and acyl-phosphatase reactions that are essential for the activation of antiviral proTides, such as Sofosbuvir and Remdesivir. hHINT1 and hHINT2 are highly homologous but exhibit disparate roles as regulators of opioid tolerance (hHINT1) and mitochondrial activity (hHINT2). NMR studies of hHINT1 reveal a pair of dynamic surface residues (Q62, E100), which gate a conserved water channel leading to the active site 13 Å away. hHINT2 crystal structures identify analogous residues (R99, D137) and water channel. hHINT1 Q62 variants significantly alter the steady-state kcat and Km for turnover of the fluorescent substrate (TpAd), while stopped-flow kinetics indicate that KD also changes. hHINT2, like hHINT1, exhibits a burst phase of adenylation, monitored by fluorescent tryptamine release, prior to rate-limiting hydrolysis and nucleotide release. hHINT2 exhibits a much smaller burst-phase amplitude than hHINT1, which is further diminished in hHINT2 R99Q. Kinetic simulations suggest that amplitude variations can be accounted for by a variable fluorescent yield of the E·S complex from changes in the environment of bound TpAd. Isothermal titration calorimetry measurements of inhibitor binding show that these hHINT variants also alter the thermodynamic binding profile. We propose that these altered surface residues engender long-range dynamic changes that affect the orientation of bound ligands, altering the thermodynamic and kinetic characteristics of hHINT active site function. Thus, studies of the cellular roles and proTide activation potential by hHINTs should consider the importance of long-range interactions and possible protein binding surfaces far from the active site.
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Affiliation(s)
- Alexander Strom
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rachit Shah
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Rafal Dolot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland
| | - Melanie S. Rogers
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455,United States
| | - Cher-Ling Tong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - David Wang
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Youlin Xia
- Department of Structural Biology, St. Jude’s Research Hospital, Memphis, Tennessee 38105, United States
| | - John D. Lipscomb
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, United States,Center for Metals in Biocatalysis, University of Minnesota, Minneapolis, Minnesota 55455,United States
| | - Carston R. Wagner
- Department of Medicinal Chemistry University of Minnesota, Minneapolis, Minnesota 55455, United States,Address correspondence to: Carston R. Wagner, University of Minnesota, Department of Medicinal Chemistry, 2231 6th Street S.E., Cancer & Cardiovascular Research Building, Minneapolis, Minnesota 55455, USA,
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8
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Subedi P, Do H, Lee JH, Oh TJ. Crystal Structure and Biochemical Analysis of a Cytochrome P450 CYP101D5 from Sphingomonas echinoides. Int J Mol Sci 2022; 23:ijms232113317. [PMID: 36362105 PMCID: PMC9655578 DOI: 10.3390/ijms232113317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Revised: 10/28/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
Cytochrome P450 enzymes (CYPs) are heme-containing enzymes that catalyze hydroxylation with a variety of biological molecules. Despite their diverse activity and substrates, the structures of CYPs are limited to a tertiary structure that is similar across all the enzymes. It has been presumed that CYPs overcome substrate selectivity with highly flexible loops and divergent sequences around the substrate entrance region. Here, we report the newly identified CYP101D5 from Sphingomonas echinoides. CYP101D5 catalyzes the hydroxylation of β-ionone and flavonoids, including naringenin and apigenin, and causes the dehydrogenation of α-ionone. A structural investigation and comparison with other CYP101 families indicated that spatial constraints at the substrate-recognition site originate from the B/C loop. Furthermore, charge distribution at the substrate binding site may be important for substrate selectivity and the preference for CYP101D5.
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Affiliation(s)
- Pradeep Subedi
- Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan 31460, Korea
| | - Hackwon Do
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Korea
| | - Jun Hyuck Lee
- Research Unit of Cryogenic Novel Material, Korea Polar Research Institute, Incheon 21990, Korea
- Department of Polar Sciences, University of Science and Technology, Incheon 21990, Korea
- Correspondence: (J.H.L.); (T.-J.O.); Tel.: +82-32-760-5555 (J.H.L.); +82-41-530-2677 (T.-J.O.); Fax: +82-32-760-5509 (J.H.L.); +82-41-530-2279 (T.-J.O.)
| | - Tae-Jin Oh
- Department of Life Science and Biochemical Engineering, Graduate School, Sun Moon University, Asan 31460, Korea
- Genome-Based BioIT Convergence Institute, Asan 31460, Korea
- Department of Pharmaceutical Engineering and Biotechnology, Sun Moon University, Asan 31460, Korea
- Correspondence: (J.H.L.); (T.-J.O.); Tel.: +82-32-760-5555 (J.H.L.); +82-41-530-2677 (T.-J.O.); Fax: +82-32-760-5509 (J.H.L.); +82-41-530-2279 (T.-J.O.)
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9
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Puławski W, Dzwolak W. Virtual Quasi-2D Intermediates as Building Blocks for Plausible Structural Models of Amyloid Fibrils from Proteins with Complex Topologies: A Case Study of Insulin. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:7024-7034. [PMID: 35617668 PMCID: PMC9178918 DOI: 10.1021/acs.langmuir.2c00699] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 05/08/2022] [Indexed: 06/15/2023]
Abstract
Conformational transitions of globular proteins into amyloid fibrils are complex multistage processes exceedingly challenging to simulate using molecular dynamics (MD). Slow monomer diffusion rates and rugged free energy landscapes disfavor swift self-assembly of orderly amyloid architectures within timescales accessible to all-atom MD. Here, we conduct a multiscale MD study of the amyloidogenic self-assembly of insulin: a small protein with a complex topology defined by two polypeptide chains interlinked by three disulfide bonds. To avoid kinetic traps, unconventional preplanarized insulin conformations are used as amyloid building blocks. These starting conformers generated through uniaxial compression of the native monomer in various spatial directions represent 6 distinct (out of 16 conceivable) two-dimensional (2D) topological classes varying in N-/C-terminal segments of insulin's A- and B-chains being placed inside or outside of the central loop constituted by the middle sections of both chains and Cys7A-Cys7B/Cys19B-Cys20A disulfide bonds. Simulations of the fibrillar self-assembly are initiated through a biased in-register alignment of two, three, or four layers of flat conformers belonging to a single topological class. The various starting topologies are conserved throughout the self-assembly process resulting in polymorphic amyloid fibrils varying in structural features such as helical twist, presence of cavities, and overall stability. Some of the protofilament structures obtained in this work are highly compatible with the earlier biophysical studies on insulin amyloid and high-resolution studies on insulin-derived amyloidogenic peptide models postulating the presence of steric zippers. Our approach provides in silico means to study amyloidogenic tendencies and viable amyloid architectures of larger disulfide-constrained proteins with complex topologies.
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Affiliation(s)
- Wojciech Puławski
- Institute
of High Pressure Physics, Polish Academy
of Sciences, 29/37 Sokołowska
Str., 01-142 Warsaw, Poland
| | - Wojciech Dzwolak
- Institute
of High Pressure Physics, Polish Academy
of Sciences, 29/37 Sokołowska
Str., 01-142 Warsaw, Poland
- Faculty
of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Str., 02-093 Warsaw, Poland
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10
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A role for the periplasmic adaptor protein AcrA in vetting substrate access to the RND efflux transporter AcrB. Sci Rep 2022; 12:4752. [PMID: 35306531 PMCID: PMC8934357 DOI: 10.1038/s41598-022-08903-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 03/14/2022] [Indexed: 11/08/2022] Open
Abstract
Tripartite resistance-nodulation-division (RND) efflux pumps, such as AcrAB-TolC of Salmonella Typhimurium, contribute to antibiotic resistance and comprise an inner membrane RND-transporter, an outer membrane factor, and a periplasmic adaptor protein (PAP). The role of the PAP in the assembly and active transport process remains poorly understood. Here, we identify the functionally critical residues involved in PAP-RND-transporter binding between AcrA and AcrB and show that the corresponding RND-binding residues in the closely related PAP AcrE, are also important for its interaction with AcrB. We also report a residue in the membrane-proximal domain of AcrA, that when mutated, differentially affects the transport of substrates utilising different AcrB efflux channels, namely channels 1 and 2. This supports a potential role for the PAP in sensing the substrate-occupied state of the proximal binding pocket of the transporter and substrate vetting. Understanding the PAP’s role in the assembly and function of tripartite RND pumps can guide novel ways to inhibit their function to combat antibiotic resistance.
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11
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Hot spots-making directed evolution easier. Biotechnol Adv 2022; 56:107926. [DOI: 10.1016/j.biotechadv.2022.107926] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 01/04/2022] [Accepted: 02/07/2022] [Indexed: 01/20/2023]
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12
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Orf GS, Gisriel CJ, Granstrom J, Baker PL, Redding KE. The PshX subunit of the photochemical reaction center from Heliobacterium modesticaldum acts as a low-energy antenna. PHOTOSYNTHESIS RESEARCH 2022; 151:11-30. [PMID: 34480322 DOI: 10.1007/s11120-021-00871-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 08/09/2021] [Indexed: 06/13/2023]
Abstract
The anoxygenic phototrophic bacterium Heliobacterium modesticaldum contains a photochemical reaction center protein complex (called the HbRC) consisting of a homodimer of the PshA polypeptide and two copies of a newly discovered polypeptide called PshX, which is a single transmembrane helix that binds two bacteriochlorophyll g molecules. To assess the function of PshX, we produced a ∆pshX strain of Hbt. modesticaldum by leveraging the endogenous Hbt. modesticaldum Type I-A CRISPR-Cas system to aid in mutant selection. We optimized this system by separating the homologous recombination and CRISPR-based selection steps into two plasmid transformations, allowing for markerless gene replacement. Fluorescence and low-temperature absorbance of the purified HbRC from the wild-type and ∆pshX strains showed that the bacteriochlorophylls bound by PshX have the lowest site energies in the entire HbRC. This indicates that PshX acts as a low-energy antenna subunit, participating in entropy-assisted uphill energy transfer toward the P800 special bacteriochlorophyll g pair. We further discuss the role that PshX may play in stability of the HbRC, its conservation in other heliobacterial species, and the evolutionary pressure to produce and maintain single-TMH subunits in similar locations in other reaction centers.
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Affiliation(s)
- Gregory S Orf
- Center for Bioenergy and Photosynthesis, School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Park, IL, 60064, USA
| | - Christopher J Gisriel
- Center for Bioenergy and Photosynthesis, School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA
| | - Jesse Granstrom
- Center for Bioenergy and Photosynthesis, School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Patricia L Baker
- Center for Bioenergy and Photosynthesis, School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | - Kevin E Redding
- Center for Bioenergy and Photosynthesis, School of Molecular Sciences, Arizona State University, Tempe, AZ, 85287, USA.
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Rostami N, Choupani E, Hernandez Y, Arab SS, Jazayeri SM, Gomari MM. SARS-CoV-2 spike evolutionary behaviors; simulation of N501Y mutation outcomes in terms of immunogenicity and structural characteristic. J Cell Biochem 2021; 123:417-430. [PMID: 34783057 PMCID: PMC8657535 DOI: 10.1002/jcb.30181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/20/2022]
Abstract
Since the emergence of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2), a large number of mutations in its genome have been reported. Some of the mutations occur in noncoding regions without affecting the pathobiology of the virus, while mutations in coding regions are significant. One of the regions where a mutation can occur, affecting the function of the virus is at the receptor‐binding domain (RBD) of the spike protein. RBD interacts with angiotensin‐converting enzyme 2 (ACE2) and facilitates the entry of the virus into the host cells. There is a lot of focus on RBD mutations, especially the displacement of N501Y which is observed in the UK/Kent, South Africa, and Brazilian lineages of SARS‐CoV‐2. Our group utilizes computational biology approaches such as immunoinformatics, protein–protein interaction analysis, molecular dynamics, free energy computation, and tertiary structure analysis to disclose the consequences of N501Y mutation at the molecular level. Surprisingly, we discovered that this mutation reduces the immunogenicity of the spike protein; also, displacement of Asn with Tyr reduces protein compactness and significantly increases the stability of the spike protein and its affinity to ACE2. Moreover, following the N501Y mutation secondary structure and folding of the spike protein changed dramatically.
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Affiliation(s)
- Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Arak, Iran
| | - Edris Choupani
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Yaeren Hernandez
- Department of Cellular and Molecular Medicine, University of Arizona, Tucson, Arizona, USA
| | - Seyed S Arab
- Department of Biophysics, School of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed M Jazayeri
- Department of Virology, School of Public Health, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad M Gomari
- Department of Medical Biotechnology, Faculty of Allied Medicine, Iran University of Medical Sciences, Tehran, Iran
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Mazur A, Grinkevich P, Chaloupkova R, Havlickova P, Kascakova B, Kuty M, Damborsky J, Kuta Smatanova I, Prudnikova T. Structural Analysis of the Ancestral Haloalkane Dehalogenase AncLinB-DmbA. Int J Mol Sci 2021; 22:ijms222111992. [PMID: 34769421 PMCID: PMC8584953 DOI: 10.3390/ijms222111992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/27/2021] [Accepted: 11/02/2021] [Indexed: 11/16/2022] Open
Abstract
Haloalkane dehalogenases (EC 3.8.1.5) play an important role in hydrolytic degradation of halogenated compounds, resulting in a halide ion, a proton, and an alcohol. They are used in biocatalysis, bioremediation, and biosensing of environmental pollutants and also for molecular tagging in cell biology. The method of ancestral sequence reconstruction leads to prediction of sequences of ancestral enzymes allowing their experimental characterization. Based on the sequences of modern haloalkane dehalogenases from the subfamily II, the most common ancestor of thoroughly characterized enzymes LinB from Sphingobium japonicum UT26 and DmbA from Mycobacterium bovis 5033/66 was in silico predicted, recombinantly produced and structurally characterized. The ancestral enzyme AncLinB-DmbA was crystallized using the sitting-drop vapor-diffusion method, yielding rod-like crystals that diffracted X-rays to 1.5 Å resolution. Structural comparison of AncLinB-DmbA with their closely related descendants LinB and DmbA revealed some differences in overall structure and tunnel architecture. Newly prepared AncLinB-DmbA has the highest active site cavity volume and the biggest entrance radius on the main tunnel in comparison to descendant enzymes. Ancestral sequence reconstruction is a powerful technique to study molecular evolution and design robust proteins for enzyme technologies.
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Affiliation(s)
- Andrii Mazur
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Pavel Grinkevich
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Radka Chaloupkova
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (R.C.); (J.D.)
- Enantis Ltd., Kamenice 771/34, 625 00 Brno, Czech Republic
| | - Petra Havlickova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Barbora Kascakova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Michal Kuty
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; (R.C.); (J.D.)
- International Clinical Research Center, St Anne’s University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Ivana Kuta Smatanova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
- Correspondence: (I.K.S.); (T.P.)
| | - Tatyana Prudnikova
- Faculty of Science, University of South Bohemia in Ceske Budejovice, Branisovska 1760, 370 05 Ceske Budejovice, Czech Republic; (A.M.); (P.G.); (P.H.); (B.K.); (M.K.)
- Correspondence: (I.K.S.); (T.P.)
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Development of an optogenetic gene sensitive to daylight and its implications in vision restoration. NPJ Regen Med 2021; 6:64. [PMID: 34650094 PMCID: PMC8516861 DOI: 10.1038/s41536-021-00177-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 09/29/2021] [Indexed: 11/14/2022] Open
Abstract
Optogenetic gene-mediated therapy for restoring vision is thought to be a useful treatment for blind patients. However, light sensitivity achieved using this gene therapy is inferior to that of daylight vision. To increase light sensitivity, we designed three mutants using a bioinformatics approach. Nucleotide sequences encoding two sites in the extracellular loops (ex1, ex3) of mVChR1 close to simulated ion-conducting pathways were replaced by homologous amino acid-encoding sequences of ChR1 or ChR2. The light sensitivity of ex3mV1 was higher than that of mVChR1 at 405–617 nm. Visual responses were restored in Royal College of Surgeons rats with genetically degenerating photoreceptor cells transfected with ex3mV1Co, wherein transmembrane of sixth (TM6) in ex3mV1 was additionally replaced with the corresponding domain of CoChR; these rats responded to light in the order of μW/mm2. Thus, ex3mV1Co might be useful for the restoration of advanced visual function.
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In silico tertiary structure prediction and evolutionary analysis of two DNA-binding proteins (DBP-1 and DBP-2) from Hyposidra talaca nucleopolyhedrovirus (HytaNPV). Biologia (Bratisl) 2021. [DOI: 10.2478/s11756-020-00665-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Mahmoudi Gomari M, Rostami N, Omidi-Ardali H, Arab SS. Insight into molecular characteristics of SARS-CoV-2 spike protein following D614G point mutation, a molecular dynamics study. J Biomol Struct Dyn 2021; 40:5634-5642. [PMID: 33475020 PMCID: PMC7832383 DOI: 10.1080/07391102.2021.1872418] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Undoubtedly, the SARS-CoV-2 has become a major concern for all societies due to its catastrophic effects on public health. In addition, mutations and changes in the structure of the virus make it difficult to design effective treatment. Moreover, the amino acid sequence of a protein is a major factor in the formation of the second and tertiary structure in a protein. Amino acid replacement can have noticeable effects on the folding of a protein, especially if an asymmetric change (substitution of polar residue with non-polar, charged with an uncharged, positive charge with a negative charge, or large residue with small residue) occurs. D614G as a spike mutant of SARS-CoV-2 previously identified as an associated risk factor with a high mortality rate of this virus. Using structural bioinformatics, our group determined that D614G mutation could cause extensive changes in SARS-CoV-2 behavior including the secondary structure, receptor binding pattern, 3D conformation, and stability of it. Communicated by Ramaswamy H. Sarma
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Affiliation(s)
| | - Neda Rostami
- Department of Chemical Engineering, Faculty of Engineering, Arak University, Iran
| | - Hossein Omidi-Ardali
- Clinical Biochemistry Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Seyed Shahriar Arab
- Department of Biophysics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
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Song W, Xu X, Gao C, Zhang Y, Wu J, Liu J, Chen X, Luo Q, Liu L. Open Gate of Corynebacterium glutamicum Threonine Deaminase for Efficient Synthesis of Bulky α-Keto Acids. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01672] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wei Song
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, P. R. China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Xin Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Yuxuan Zhang
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Jing Wu
- School of Pharmaceutical Science, Jiangnan University, Wuxi 214122, P. R. China
| | - Jia Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Qiuling Luo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi 214122, P. R. China
- Key Laboratory of Industrial Biotechnology, Ministry of Education, Jiangnan University, Wuxi 214122, P. R. China
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Kokkonen P, Bednar D, Pinto G, Prokop Z, Damborsky J. Engineering enzyme access tunnels. Biotechnol Adv 2019; 37:107386. [PMID: 31026496 DOI: 10.1016/j.biotechadv.2019.04.008] [Citation(s) in RCA: 107] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 04/16/2019] [Accepted: 04/18/2019] [Indexed: 12/14/2022]
Abstract
Enzymes are efficient and specific catalysts for many essential reactions in biotechnological and pharmaceutical industries. Many times, the natural enzymes do not display the catalytic efficiency, stability or specificity required for these industrial processes. The current enzyme engineering methods offer solutions to this problem, but they mainly target the buried active site where the chemical reaction takes place. Despite being many times ignored, the tunnels and channels connecting the environment with the active site are equally important for the catalytic properties of enzymes. Changes in the enzymatic tunnels and channels affect enzyme activity, specificity, promiscuity, enantioselectivity and stability. This review provides an overview of the emerging field of enzyme access tunnel engineering with case studies describing design of all the aforementioned properties. The software tools for the analysis of geometry and function of the enzymatic tunnels and channels and for the rational design of tunnel modifications will also be discussed. The combination of new software tools and enzyme engineering strategies will provide enzymes with access tunnels and channels specifically tailored for individual industrial processes.
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Affiliation(s)
- Piia Kokkonen
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - David Bednar
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Gaspar Pinto
- International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic; International Clinical Research Center, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic.
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20
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Briones R, Blau C, Kutzner C, de Groot BL, Aponte-Santamaría C. GROmaρs: A GROMACS-Based Toolset to Analyze Density Maps Derived from Molecular Dynamics Simulations. Biophys J 2018; 116:4-11. [PMID: 30558883 DOI: 10.1016/j.bpj.2018.11.3126] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 11/19/2018] [Accepted: 11/26/2018] [Indexed: 12/31/2022] Open
Abstract
We introduce a computational toolset, named GROmaρs, to obtain and compare time-averaged density maps from molecular dynamics simulations. GROmaρs efficiently computes density maps by fast multi-Gaussian spreading of atomic densities onto a three-dimensional grid. It complements existing map-based tools by enabling spatial inspection of atomic average localization during the simulations. Most importantly, it allows the comparison between computed and reference maps (e.g., experimental) through calculation of difference maps and local and time-resolved global correlation. These comparison operations proved useful to quantitatively contrast perturbed and control simulation data sets and to examine how much biomolecular systems resemble both synthetic and experimental density maps. This was especially advantageous for multimolecule systems in which standard comparisons like RMSDs are difficult to compute. In addition, GROmaρs incorporates absolute and relative spatial free-energy estimates to provide an energetic picture of atomistic localization. This is an open-source GROMACS-based toolset, thus allowing for static or dynamic selection of atoms or even coarse-grained beads for the density calculation. Furthermore, masking of regions was implemented to speed up calculations and to facilitate the comparison with experimental maps. Beyond map comparison, GROmaρs provides a straightforward method to detect solvent cavities and average charge distribution in biomolecular systems. We employed all these functionalities to inspect the localization of lipid and water molecules in aquaporin systems, the binding of cholesterol to the G protein coupled chemokine receptor type 4, and the identification of permeation pathways through the dermicidin antimicrobial channel. Based on these examples, we anticipate a high applicability of GROmaρs for the analysis of molecular dynamics simulations and their comparison with experimentally determined densities.
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Affiliation(s)
- Rodolfo Briones
- Computational Neurophysiology Group, Institute of Complex Systems 4, Forschungszentrum Jülich, Jülich, Germany
| | - Christian Blau
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholms Universitet, Stockholm, Sweden
| | - Carsten Kutzner
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Bert L de Groot
- Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Camilo Aponte-Santamaría
- Max Planck Tandem Group in Computational Biophysics, University of Los Andes, Bogotá, Colombia; Interdisciplinary Center for Scientific Computing, Heidelberg University, Heidelberg, Germany.
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